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FGF3
Final classification
VUS
FGF3 c.351del · p.Phe117LeufsTer41
FGF3

NM_005247.2:c.351del is a frameshift variant in exon 3 of 3 of FGF3 predicted to produce a truncated protein p.(Phe117LeufsTer41) with loss of the C-terminal 83 amino acids. PVS1 is applied at moderate strength under the ClinGen SVI framework (PMC6185798), downgraded from full strength due to location in the last exon with predicted NMD escape.

Gene
FGF3
Transcript
NM_005247.2
HGVS · transcript:coding
NM_005247.2:c.351del
Consequence
N/A
GRCh38
chr11:69810673 CA>C
GRCh37
chr11:69625441 CA>C
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PVS1 moderate, PM2 moderate; combination = 2 moderate, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PVS1 moderate, PM2 moderate; combination = 2 moderate, which maps to VUS.
Classification rationale
PVS1PM2 VUS
FGF3 c.351del

NM_005247.2:c.351del is a frameshift variant in exon 3 of 3 of FGF3 predicted to produce a truncated protein p.(Phe117LeufsTer41) with loss of the C-terminal 83 amino acids. PVS1 is applied at moderate strength under the ClinGen SVI framework (PMC6185798), downgraded from full strength due to location in the last exon with predicted NMD escape.1 This variant is absent from all population databases including gnomAD v2.1, v4.1, and gnomAD-Canada (allele frequency 0.00%), meeting PM2 at moderate strength.2 The variant is absent from ClinVar and has not been reported in the literature or somatic cancer databases (COSMIC). No functional studies, de novo observations, case-control data, or cosegregation evidence are available.3 With two moderate pathogenic criteria (PVS1_Moderate, PM2_Moderate) and no benign criteria met, the evidence does not reach the threshold for Likely Pathogenic under generic ACMG/AMP 2015 rules (requires three moderate or two moderate plus two supporting criteria). This variant is classified as a Variant of Uncertain Significance (VUS). Additional evidence from functional studies, clinical observations, or family segregation data would be required to reclassify this variant.4

PVS1 + PM2 VUS
Gene diagram · NM_005247.2 · variants mapped to exon structure
FGF3 NM_005247.2
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 16 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PVS1 moderate review Pathogenic
NM_005247.2:c.351del is a frameshift variant in exon 3 of 3 (the last exon) predicted to result in a truncated protein p.(Phe117LeufsTer41) with loss of approximately 35% of the C-terminal protein sequence and addition of 41 aberrant amino acids. FGF3 loss of function is supported as a germline disease mechanism (BOR syndrome candidate gene; PMID:23851940). Under ClinGen SVI PVS1 recommendations (PMC6185798), frameshift variants in the last exon are predicted to escape nonsense-mediated decay, which warrants a strength downgrade. The removed C-terminal region is substantial but its specific functional criticality has not been characterized in the evidence reviewed. PVS1 is applied at moderate strength given the established gene-level LoF mechanism tempered by NMD escape and uncertain functional domain characterization of the truncated region.
Frameshift variant in last exon (3/3) of FGF3predicted to escape NMD under PMC6185798p.(Phe117LeufsTer41) removes ~83 C-terminal amino acids (35% of protein) and replaces with 41 aberrant residues
PM2 moderate Pathogenic
This variant is completely absent from all population databases (gnomAD v2.1, gnomAD v4.1, gnomAD-Canada v1.0), with an observed allele frequency of 0.00%. Under the generic ACMG/AMP framework, absence from large population cohorts at a frequency below 0.1% satisfies PM2 at moderate strength.
Absent from gnomAD v2.1 (0 alleles observed)Absent from gnomAD v4.1 (0 alleles observed)Absent from gnomAD-Canada v1.0 (0 alleles observed)
Assessed · not applied
Pathogenic
PS2 No de novo data are available for this variant.
PS3 No functional studies testing this exact variant or a systematically characterized range that includes position 117 were identified.
PS4 The variant is absent from ClinVar and population databases.
PM1 The variant does not lie in a statistically significant mutational hotspot per cancerhotspots.org, and no specific functional domain characterization data for the FGF3 C-terminal region at position 117 is available in the case evidence to support a PM1 application at domain level.
PM6 No de novo observation has been reported for this variant.
PP1 No cosegregation data are available for this variant.
PP4 No patient phenotype or clinical data are available in the case evidence.
PP5 This variant is absent from ClinVar.
Benign
BA1 BA1 requires an allele frequency greater than 1% in population databases.
BS1 BS1 requires an allele frequency greater than 0.3% in population databases for non-VCEP assessment.
BS2 BS2 requires observation of the variant in a healthy adult individual (for fully penetrant disorders) or in trans with a pathogenic variant (for recessive disorders).
BS3 BS3 requires well-established functional studies demonstrating no deleterious effect.
BS4 BS4 requires lack of segregation with disease in affected family members.
BP2 BP2 requires observation in trans with a pathogenic variant in a gene associated with a recessive disorder, or in cis with a pathogenic variant in a dominant disorder.
BP5 BP5 requires observation of the variant in a case with an alternate molecular basis for disease.
BP6 This variant is absent from ClinVar.
N/A · 10 PS1 · PM3 · PM4 · PM5 · PP2 · PP3 · BP1 · BP3 · BP4 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots